They could've negotiated with Carl. Tell him they'd surrender, cede the floor, and give all the crawlers token contracts to get out of the dungeon in exchange for letting them all live and letting the crawl end. Maybe sign contracts guaranteeing it. I think that's better than the alternative of dealing with the psychotic AI trapping them in the system, a death match with Carl, and shooting each other in orbit. Just blow through the ascendancy that kicks off right after, get in their ships, and GTFO.
The AI might see it as a ***** move, but it's still bound by all the rules.